Comparing modeling methods of genomic prediction for growth traits of a tropical timber species, Shorea macrophylla

IntroductionShorea macrophylla is a commercially important tropical tree species grown for timber and oil. It is amenable to plantation forestry due to its fast initial growth. Genomic selection (GS) has been used in tree breeding studies to shorten long breeding cycles but has not previously been applied to S. macrophylla.MethodsTo build genomic prediction models for GS, leaves and growth trait data were collected from a half-sib progeny population of S. macrophylla in Sari Bumi Kusuma forest concession, central Kalimantan, Indonesia. 18037 SNP markers were identified in two ddRAD-seq libraries. Genomic prediction models based on these SNPs were then generated for diameter at breast height and total height in the 7th year from planting (D7 and H7).Results and discussionThese traits were chosen because of their relatively high narrow-sense genomic heritability and because seven years was considered long enough to assess initial growth. Genomic prediction models were built using 6 methods and their derivatives with the full set of identified SNPs and subsets of 48, 96, and 192 SNPs selected based on the results of a genome-wide association study (GWAS). The GBLUP and RKHS methods gave the highest predictive ability for D7 and H7 with the sets of selected SNPs and showed that D7 has an additive genetic architecture while H7 has an epistatic genetic architecture. LightGBM and CNN1D also achieved high predictive abilities for D7 with 48 and 96 selected SNPs, and for H7 with 96 and 192 selected SNPs, showing that gradient boosting decision trees and deep learning can be useful in genomic prediction. Predictive abilities were higher in H7 when smaller number of SNP subsets selected by GWAS p-value was used, However, D7 showed the contrary tendency, which might have originated from the difference in genetic architecture between primary and secondary growth of the species. This study suggests that GS with GWAS-based SNP selection can be used in breeding for non-cultivated tree species to improve initial growth and reduce genotyping costs for next-generation seedlings

Production and nonclinical evaluation of an autologous iPSC-derived platelet product for the iPLAT1 clinical trial

血小板減少症に対するiPS細胞由来血小板の自己輸血に関する臨床研究」の成果公表（論文発表）について. 京都大学プレスリリース. 2022-09-30.Donor-derived platelets are used to treat or prevent hemorrhage in patients with thrombocytopenia. However, ∼5% or more of these patients are complicated with alloimmune platelet transfusion refractoriness (allo-PTR) due to alloantibodies against HLA-I or human platelet antigens (HPA). In these cases, platelets from compatible donors are necessary, but it is difficult to find such donors for patients with rare HLA-I or HPA. To produce platelet products for patients with aplastic anemia with allo-PTR due to rare HPA-1 mismatch in Japan, we developed an ex vivo good manufacturing process (GMP)–based production system for an induced pluripotent stem cell–derived platelet product (iPSC-PLTs). Immortalized megakaryocyte progenitor cell lines (imMKCLs) were established from patient iPSCs, and a competent imMKCL clone was selected for the master cell bank (MCB) and confirmed for safety, including negativity of pathogens. From this MCB, iPSC-PLTs were produced using turbulent flow bioreactors and new drugs. In extensive nonclinical studies, iPSC-PLTs were confirmed for quality, safety, and efficacy, including hemostasis in a rabbit model. This report presents a complete system for the GMP-based production of iPSC-PLTs and the required nonclinical studies and thus supports the iPLAT1 study, the first-in-human clinical trial of iPSC-PLTs in a patient with allo-PTR and no compatible donor using the autologous product. It also serves as a comprehensive reference for the development of widely applicable allogeneic iPSC-PLTs and other cell products that use iPSC-derived progenitor cells as MCB

Molecular database for classifying Shorea species (Dipterocarpaceae) and techniques for checking the legitimacy of timber and wood products

The extent of tropical forest has been declining, due to over-exploitation and illegal logging activities. Large quantities of unlawfully extracted timber and other wood products have been exported, mainly to developed countries. As part of the export monitoring effort, we have developed methods for extracting and analyzing DNA from wood products, such as veneers and sawn timbers made from dipterocarps, in order to identify the species from which they originated. We have also developed a chloroplast DNA database for classifying Shorea species, which are both ecologically and commercially important canopy tree species in the forests of Southeast Asia. We are able to determine the candidate species of wood samples, based on DNA sequences and anatomical data. The methods for analyzing DNA from dipterocarp wood products may have strong deterrent effects on international trade of illegitimate dipterocarp products. However, the method for analyzing DNA from wood is not perfect for all wood products and need for more improvement, especially for plywood sample. Consequently, there may be benefits for the conservation of tropical forests in Southeast Asia. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10265-010-0348-z) contains supplementary material, which is available to authorized users

Physical performance disorder（Locomotive syndrome）closely relates to both hypertension and diabetes mellitus which are components of metabolic syndrome

Locomotive syndrome is physical performance disorder in the elderly person. The physical performance disorder can become cause of metabolic syndrome. This study focused on the locomotive syndrome’s relationship to the hypertension, diabetes mellitus, and hyperlipidemia which are components of the metabolic syndrome. To evaluate the locomotive syndrome, questionnaire score system : brand-new loco-check-score and established locomo-５-score were adopted. In the questionnaire, current medications were also listed especially about hypertension, diabetes mellitus, and hyperlipidemia. A correlation between loco-check-score and locomo-５-score was statistically evaluated by Spearman rank correlation coefficient. Moreover correlations between body mass index（BMI）and loco-check-score, BMI and locomo-５-score were statistically evaluated by Spearman rank correlation coefficient. In a health consultation event, １４６ persons checked the questionnaire （mean age ７２．５yo）. Differences of the loco-check-score and the locomo-５-score in the hypertension-group, diabetes mellitus group, and the hyperlipidemia group were statistically evaluated by the Mann-Whitney U test respectively. Age matched persons with no medications comprised control groups. Significant differences were observed in the hypertension group and diabetes mellitus group both in the loco-check-score and locomo-５-score systems. These two groups showed significantly high loco-check-score and locomo-５-score than the control groups. The loco-check-score closely related to the locomo-５-score. On the other hand, no relations were observed between BMI and the loco-check-score, and between BMI and the locomo-５-score